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dc.contributor.authorButtler, Jeremy B.
dc.date.accessioned2022-12-17T23:27:52Z
dc.date.available2022-12-17T23:27:52Z
dc.date.issued2022-08
dc.identifier.urihttp://hdl.handle.net/11122/13071
dc.descriptionThesis (M.S.) University of Alaska Fairbanks, 2022en_US
dc.description.abstractOne Health is the concept of interconnected health between plants, animals, humans, microorganisms and the environments they live in. One Health issues surround many important viral pathogens, including influenza, SARS-CoV-2, and Ebola, that have likely come from zoonotic spillovers. Genomic epidemiology combines pathogen genomes with metadata to forecast, track, and prepare for future pathogens and pathogen variants that may cause epidemics. Genomic epidemiology has been used to detect and track viral variants that have the potential to escape vaccines for viruses like porcine circovirus type 2 (PCV2). PCV2 causes porcine circovirus associated diseases (PCVAD), which results in weight loss and death in pigs around the world. The correlation between PCVAD and mixed infections shows that disease severity is linked to the microbial community in a host. Metagenomics allows researchers to sequence samples and sort out the individual community member genomes by bioinformatic analyses, allowing the study of the host microbiome. In this thesis, I tested if long read nanopore sequencing can uncover PCV2 diversity and reliably detect co-infections. I also assessed the accuracy and efficiency of long read metagenomic assemblers as a potential method for detecting mixed infections. In my first chapter, I found that nanopore sequencing can be used to understand PCV2 diversity and detect co-infections. This evidence shows that nanopore sequencing is a viable alternative to Sanger sequencing for PCV2 surveillance. In my second chapter, I found Flye built the most complete and accurate genomes for bacterial community members and their plasmids. Throughout my thesis I have shown that nanopore sequencing is a viable solution for modern surveillance. The lower cost of nanopore sequencing may allow more specific pathogen and metagenomic surveillance in regions with high risk of zoonotic spillovers, which may allow early detection of epidemic causing pathogens.en_US
dc.description.sponsorshipNational Institute of General Medical Sciences of the National Institutes of Health under awards UL1GM118991, TL4GM118992, RL5GM118990, Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant 2P20GM103395en_US
dc.description.tableofcontentsGeneral introduction. Chapter 1: Genetic diversity of porcine circovirus 2 in wild boars and domestic pigs in Ukraine. Chapter 2: Accuracy and completeness of long read metagenomic assemblies. General Conclusions -- Appendix.en_US
dc.language.isoen_USen_US
dc.subjectPathogenic microorganismsen_US
dc.subjectMicrobial genomicsen_US
dc.subjectMetagenomicsen_US
dc.subjectCircovirusesen_US
dc.subjectCircovirus detectionen_US
dc.subjectCircovirus monitoringen_US
dc.subjectSwine diseasesen_US
dc.subjectUkraineen_US
dc.subject.otherMaster of Science in Biological Sciencesen_US
dc.titleApplying third-generation sequencing to pathogen surveillance and mixed infection detectionen_US
dc.typeThesisen_US
dc.type.degreemsen_US
dc.identifier.departmentDepartment of Biology and Wildlifeen_US
dc.contributor.chairDrown, Devin M.
dc.contributor.chairBortz, Eric
dc.contributor.committeeTakebayashi, Naoki
dc.contributor.committeeMurphy, Molly
refterms.dateFOA2022-12-17T23:27:52Z


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